Assistance with Minian final Merge option

[Ella Hanzin]

Hi all,

I’m reaching out for help with using the merge option in Minian. I’ve successfully run Minian and reached the stage where I can manually merge cells. However, I’ve encountered an issue with saving the merged data.

After completing the merge, when I try to save the dataset using minian_ds.to_netcdf("minian_dataset.nc"), the saved data appears as null. Upon inspecting the dataset, it seems that the merge process isn’t fully combining the cells—it retains the original data and only updates the unit labels.

This doesn’t seem to align with how the merge is supposed to function. I’m aiming to save the final, cleaned dataset with the merges fully applied.

Could you please advise on how to resolve this issue?

Best regards,
Ella

[Ariel Cohen]

Hi Ella,

Indeed, it seems that the corrected unit_id labels from the manual merging/deleting step in the CNMF section are just assigned as unit labels, not their unit_id values, and that deleted cells are labelled as "-1." I have also noticed gaps in the unit_ids from cells removed throughout the pipeline before this final step. I have solved these issues by assigning cnmfviewer unit_labels as unit_id values (not unit_labels), removing deleted cells (those with negative unit_ids), and then relabelling all retained cells from 0 to len(C.unit_id). 

I have attached my version of the minian pipeline notebook below for your reference. Hope this helps!

Ariel